option to validate hmm hits by sequence score

BIONF · Dec 20, 2023 · e1f92f1 · e1f92f1
1 parent 0404231
commit e1f92f1
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/fdog/runMulti.py b/fdog/runMulti.py
@@ -368,7 +368,7 @@ def main():
  coreArgs = [minDist, maxDist, coreSize, coreTaxa, distDeviation,
  alnStrategy, fasOff]
  orthoCoreArgs = [CorecheckCoorthologsOff, rbh, True, evalBlast/10,
- lowComplexityFilter, evalHmmer/10, coreHitLimit,
+ lowComplexityFilter, evalHmmer/10, coreHitLimit, hmmScoreType,
  scoreCutoff, aligner] # rep = True; e-value cutoff is 10x more stringent than from ortho search
  otherCoreArgs = [cpus, debugCore, silentOff, noCleanup, force, append]
  core_options = [coreArgs, orthoCoreArgs, otherCoreArgs]

diff --git a/fdog/runSingle.py b/fdog/runSingle.py
@@ -239,7 +239,7 @@ def main():
  coreArgs = [minDist, maxDist, coreSize, coreTaxa, distDeviation,
  alnStrategy, fasOff]
  orthoCoreArgs = [CorecheckCoorthologsOff, rbh, True, evalBlast/10,
- lowComplexityFilter, evalHmmer/10, coreHitLimit,
+ lowComplexityFilter, evalHmmer/10, coreHitLimit, hmmScoreType,
  scoreCutoff, aligner] # rep = True; e-value cutoff is 10x more stringent than from ortho search
  otherCoreArgs = [cpus, debugCore, silentOff, noCleanup, force, append]
  print('##### COMPILING CORE SET FOR %s #####' % seqName)